Advanced electrode models and numerical modelling for high frequency Electrical Impedance Tomography systems

The thesis discusses various electrode models and finite element analysis methods for Electrical Impedance Tomography (EIT) systems. EIT is a technique for determining the distribution of the conductivity or admittivity in a volume by injecting electrical currents into the volume and measuring the corresponding potentials on the surface of the volume. Various electrode models were investigated for operating EIT systems at higher frequencies in the beta-dispersion band. Research has shown that EIT is potentially capable to distinguish malignant and benign tumours in this frequency band. My study concludes that instrumental effects of the electrodes and full Maxwell effects of EIT systems are the major issues, and they have to be addressed when the operating frequency increases. In the thesis, I proposed 1) an Instrumental Electrode Model (IEM) for the quasi-static EIT formula, based on the analysis of the hardware structures attached to electrodes; 2) a Complete Electrode Model based on Impedance Boundary Conditions (CEM-IBC) that introduces the contact impedances into the full Maxwell EIT formula; 3) a Transmission line Port Model (TPM) for electrode pairs with the instrumental effects, the contact impedance, and the full Maxwell effects considered for EIT systems. Circuit analysis, Partial Differential Equations (PDE) analysis, numerical analysis and finite element methods were used to develop the models. The results obtained by the proposed models are compared with widely used Commercial PDE solvers. This thesis addresses the two major problems (instrumental effects of the electrodes and full Maxwell effects of EIT systems) with the proposed advanced electrode models. Numerical experiments show that the proposed models are more accurate in the high frequency range of EIT systems. The proposed electrode models can be also applicable to inverse problems, and the results show promising. Simple hardware circuits for verifying the results experimentally have been also designed

Graph-Based Decoding Model for Functional Alignment of Unaligned fMRI Data

Aggregating multi-subject functional magnetic resonance imaging (fMRI) data is indispensable for generating valid and general inferences from patterns distributed across human brains. The disparities in anatomical structures and functional topographies of human brains warrant aligning fMRI data across subjects. However, the existing functional alignment methods cannot handle well various kinds of fMRI datasets today, especially when they are not temporally-aligned, i.e., some of the subjects probably lack the responses to some stimuli, or different subjects might follow different sequences of stimuli. In this paper, a cross-subject graph that depicts the (dis)similarities between samples across subjects is used as a priori for developing a more flexible framework that suits an assortment of fMRI datasets. However, the high dimension of fMRI data and the use of multiple subjects makes the crude framework time-consuming or unpractical. To address this issue, we further regularize the framework, so that a novel feasible kernel-based optimization, which permits nonlinear feature extraction, could be theoretically developed. Specifically, a low-dimension assumption is imposed on each new feature space to avoid overfitting caused by the highspatial-low-temporal resolution of fMRI data. Experimental results on five datasets suggest that the proposed method is not only superior to several state-of-the-art methods on temporally-aligned fMRI data, but also suitable for dealing `with temporally-unaligned fMRI data.Comment: 17 pages, 10 figures, Proceedings of the Association for the Advancement of Artificial Intelligence (AAAI-20

Systemic similarity analysis of compatibility drug-induced multiple pathway patterns _in vivo_

A major challenge in post-genomic research is to understand how physiological and pathological phenotypes arise from the networks of expressed genes and to develop powerful tools for translating the information exchanged between gene and the organ system networks. Although different expression modules may contribute independently to different phenotypes, it is difficult to interpret microarray experimental results at the level of single gene associations. The global effects and response pathways of small molecules in cells have been investigated, but the quantitative details of the activation mechanisms of multiple pathways _in vivo_ are not well understood. Similar response networks indicate similar modes of action, and gene networks may appear to be similar despite differences in the behaviour of individual gene groups. Here we establish the method for assessing global effect spectra of the complex signaling forms using Global Similarity Index (GSI) in cosines vector included angle. Our approach provides quantitative multidimensional measures of genes expression profile based on drug-dependent phenotypic alteration _in vivo_. These results make a starting point for identifying relationships between GSI at the molecular level and a step toward phenotypic outcomes at a system level to predict action of unknown compounds and any combination therapy

Development of Estrogen Receptor Beta Binding Prediction Model Using Large Sets of Chemicals

We developed an ERβ binding prediction model to facilitate identification of chemicals specifically bind ERβ or ERα together with our previously developed ERα binding model. Decision Forest was used to train ERβ binding prediction model based on a large set of compounds obtained from EADB. Model performance was estimated through 1000 iterations of 5-fold cross validations. Prediction confidence was analyzed using predictions from the cross validations. Informative chemical features for ERβ binding were identified through analysis of the frequency data of chemical descriptors used in the models in the 5-fold cross validations. 1000 permutations were conducted to assess the chance correlation. The average accuracy of 5-fold cross validations was 93.14% with a standard deviation of 0.64%. Prediction confidence analysis indicated that the higher the prediction confidence the more accurate the predictions. Permutation testing results revealed that the prediction model is unlikely generated by chance. Eighteen informative descriptors were identified to be important to ERβ binding prediction. Application of the prediction model to the data from ToxCast project yielded very high sensitivity of 90-92%. Our results demonstrated ERβ binding of chemicals could be accurately predicted using the developed model. Coupling with our previously developed ERα prediction model, this model could be expected to facilitate drug development through identification of chemicals that specifically bind ERβ or ERα